MolNFT v1 · #25497 · protein + DNA
Co-crystal structure of the hnf-3/FORK head DNA-recognition motif resembles histone H5
1VTN · DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3'): “Co-crystal structure of the hnf-3/FORK head DNA-recognition motif resembles histone H5”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.47). MolNFT v1 #25497…
- PDB
- 1VTN
- Type
- protein + DNA
- Length
- 128 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3'); DNA…
- UniProt
- P55318
- Ligands
- MG
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3') | dna | 13 | — | — |
| B | DNA (5'-D(*GP*GP*TP*TP*GP*AP*CP*TP*TP*AP*GP*TP*C)-3') | dna | 13 | — | — |
| C | Hnf-3/FORK head DNA-recognition motif | protein | 102 | 41% helix, 9% strand | P55318 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.47 | 0.80 | 15 | empty |
| 2 | 51 | 0.45 | 0.85 | 18 | empty |
| 3 | 63 | 0.28 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–C · 618 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 569 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- B–C · 539 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1VTN · Co-crystal structure of the hnf-3/FORK head DNA-recognition motif resembles histone H5 · the same entry in another collection · chain A against A, TM-score 1.00
- P55318 · AlphaFold monomer V2.0 prediction for hepatocyte nuclear factor 3-gamma (P55318) · a predicted model of the same protein · chain C against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P55318
- Elsewhere: RCSB PDB 1VTN · PDBe 1VTN · UniProt P55318
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.